Thermodynamic integration questions

From: Randall Hall (
Date: Thu Jan 09 2014 - 12:16:03 CST

  After looking at the available documentation and searching the namd-l list, I have a couple of clarification questions:

1) I am mutating a charged residue into another charged residue with the same overall charge. Do I also need to mutate one set of counterions into another set of counterions or can I use a single set of counterions that does not appear or disappear?

2) I am using the TI job type. The output states that what is reported in the alch output file is dU/dlambda for both the type 1 and type 2 particles. I believe this means that I must subtract the two entries to form the Delta A integrand. Is this correct?


Randall Hall
Lillian L.Y. Wang Yin, Ph.D. Endowed Professor of Chemistry
Chair, Department of Natural Sciences and Mathematics
Dominican University of California
Phone: 415-482-1911
Fax: 415-482-1972

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